function varargout = CellTrackerSettingsGeneral(varargin) % CELLTRACKERSETTINGSGENERAL M-file for CellTrackerSettingsGeneral.fig % CELLTRACKERSETTINGSGENERAL, by itself, creates a new CELLTRACKERSETTINGSGENERAL or raises the existing % singleton*. % % H = CELLTRACKERSETTINGSGENERAL returns the handle to a new CELLTRACKERSETTINGSGENERAL or the handle to % the existing singleton*. % % CELLTRACKERSETTINGSGENERAL('CALLBACK',hObject,eventData,handles,...) calls the local % function named CALLBACK in CELLTRACKERSETTINGSGENERAL.M with the given input arguments. % % CELLTRACKERSETTINGSGENERAL('Property','Value',...) creates a new CELLTRACKERSETTINGSGENERAL or raises the % existing singleton*. Starting from the left, property value pairs are % applied to the GUI before CellTrackerSettingsGeneral_OpeningFcn gets called. An % unrecognized property name or invalid value makes property application % stop. All inputs are passed to CellTrackerSettingsGeneral_OpeningFcn via varargin. % % *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one % instance to run (singleton)". % % See also: GUIDE, GUIDATA, GUIHANDLES % Edit the above text to modify the response to help CellTrackerSettingsGeneral % Last Modified by GUIDE v2.5 26-Jun-2015 16:36:13 % Begin initialization code - DO NOT EDIT gui_Singleton = 1; gui_State = struct('gui_Name', mfilename, ... 'gui_Singleton', gui_Singleton, ... 'gui_OpeningFcn', @CellTrackerSettingsGeneral_OpeningFcn, ... 'gui_OutputFcn', @CellTrackerSettingsGeneral_OutputFcn, ... 'gui_LayoutFcn', [] , ... 'gui_Callback', []); if nargin && ischar(varargin{1}) gui_State.gui_Callback = str2func(varargin{1}); end if nargout [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); else gui_mainfcn(gui_State, varargin{:}); end % End initialization code - DO NOT EDIT % --- Executes just before CellTrackerSettingsGeneral is made visible. function CellTrackerSettingsGeneral_OpeningFcn(hObject, eventdata, handles, varargin) % This function has no output args, see OutputFcn. % hObject handle to figure % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) % varargin command line arguments to CellTrackerSettingsGeneral (see VARARGIN) global f_handles % Choose default command line output for CellTrackerSettingsGeneral handles.output = hObject; % Update handles structure guidata(hObject, handles); % UIWAIT makes CellTrackerSettingsGeneral wait for user response (see UIRESUME) % uiwait(handles.figure1); %% set parameters to show try % Close the other windows %if ishandle(f_handles.h_GUIsetG); close(f_handles.h_GUIsetG); end; if ishandle(f_handles.h_GUIsetT); close(f_handles.h_GUIsetT); end; if ishandle(f_handles.h_GUIsetS); close(f_handles.h_GUIsetS); end; if ishandle(f_handles.h_GUIsetM); close(f_handles.h_GUIsetM); end; if ishandle(f_handles.h_GUIstatistics); close(f_handles.h_GUIstatistics); end; inpImage = imread(f_handles.PathImgOriginal, 1); [rowI, colI, chI] = size(inpImage); numImages = length(imfinfo(f_handles.PathImgOriginal)); % background correction if f_handles.backCorrMethod == 1 set(handles.radiobutton1, 'Value', 1); elseif f_handles.backCorrMethod == 2 set(handles.radiobutton2, 'Value', 1); end; % Check parameters if f_handles.backCorrSize<1 || f_handles.backCorrSize>=min([rowI, colI]) f_handles.backCorrSize = 1; end if f_handles.maxAlignDistance<0 || f_handles.maxAlignDistance>=min([rowI, colI]) f_handles.maxAlignDistance = ceil(min([rowI, colI])/10); end % Set parameters set(handles.edit1, 'String', num2str(f_handles.backCorrSize)); % auto aligner set(handles.edit3, 'String', num2str(f_handles.maxAlignDistance)); catch ME1 Message = {'Wrong parameter set.', ... ' '}; msgbox(Message,'Message') end % --- Outputs from this function are returned to the command line. function varargout = CellTrackerSettingsGeneral_OutputFcn(hObject, eventdata, handles) % varargout cell array for returning output args (see VARARGOUT); % hObject handle to figure % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) % Get default command line output from handles structure varargout{1} = handles.output; % --- Executes during object deletion, before destroying properties. function figure1_DeleteFcn(hObject, eventdata, handles) % hObject handle to figure1 (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) % --- Executes when user attempts to close figure1. function figure1_CloseRequestFcn(hObject, eventdata, handles) % hObject handle to figure1 (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) % Hint: delete(hObject) closes the figure delete(hObject); % --- Executes on button press in pb_saveSettings. function pb_saveSettings_Callback(hObject, eventdata, handles) % hObject handle to pb_saveSettings (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) %% OK button to save settings global f_handles; try %Reset input f_handles.PathImgCurrent = f_handles.PathImgOriginal; f_handles.startIm = 1; f_handles.lastImage = length(imfinfo(f_handles.PathImgOriginal)); % Errors check inpImage = imread(f_handles.PathImgCurrent, 1); [rowI, colI, chI] = size(inpImage); numImages = length(imfinfo(f_handles.PathImgCurrent)); testBackCorrSize = str2num(get(handles.edit1, 'String')); testMaxAlignDistance = str2num(get(handles.edit3, 'String')); flag_ComputationOn = 1; if testBackCorrSize<1 || testBackCorrSize>=min([rowI, colI]) flag_ComputationOn = 0; end if testMaxAlignDistance<0 || testMaxAlignDistance>=min([rowI, colI]) flag_ComputationOn = 0; end if flag_ComputationOn == 1 if get(handles.radiobutton1, 'Value')== 1 f_handles.backCorrMethod = 1; elseif get(handles.radiobutton2, 'Value') == 1 f_handles.backCorrMethod = 2; end; f_handles.backCorrSize = str2num(get(handles.edit1, 'String')); % auto aligner f_handles.maxAlignDistance = str2num(get(handles.edit3, 'String')); % Reset GUI set(f_handles.h_FCpb02, 'BackgroundColor', 'yellow'); set(f_handles.h_FCpb03, 'BackgroundColor', 'yellow'); set(f_handles.h_FCpb04, 'BackgroundColor', 'yellow'); set(f_handles.h_FCpb05, 'BackgroundColor', 'yellow'); set(f_handles.h_FCpb06, 'BackgroundColor', 'yellow'); set(f_handles.h_FCpb07, 'BackgroundColor', 'red'); % Update visualization % Save output path = [pwd filesep 'tmpct' filesep]; fileNameMat = 'TracksCoordinates.mat'; fileNameExcel = 'TracksCoordinates.xls'; pathFileNameMat = [path fileNameMat]; pathFileNameExcel = [path fileNameExcel]; if ~isempty(f_handles.pos) pos = f_handles.pos; if isequal(exist(pathFileNameMat, 'file'),2); delete(pathFileNameMat); save(pathFileNameMat, 'pos'); else save(pathFileNameMat, 'pos'); end; if isequal(exist(pathFileNameExcel, 'file'),2); delete(pathFileNameExcel); xlswrite(pathFileNameExcel, pos); else xlswrite(pathFileNameExcel, pos); end; f_handles.pos = []; else if isequal(exist(pathFileNameMat, 'file'),2); delete(pathFileNameMat); end; if isequal(exist(pathFileNameExcel, 'file'),2); delete(pathFileNameExcel); end; end f_handles.PathImgCurrent = f_handles.PathImgOriginal; guidata(hObject, handles); updateSliceWindows(f_handles.startIm, f_handles.PathImgCurrent, handles); if ishandle(f_handles.h_GUIsetG); close(f_handles.h_GUIsetG); end; else Message = {'Wrong parameter set.', ... ' '}; msgbox(Message,'Message') end catch ME1 Message = {'Wrong parameter set.', ... ' '}; msgbox(Message,'Message') end function edit1_Callback(hObject, eventdata, handles) % hObject handle to edit1 (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) % Hints: get(hObject,'String') returns contents of edit1 as text % str2double(get(hObject,'String')) returns contents of edit1 as a double % --- Executes during object creation, after setting all properties. function edit1_CreateFcn(hObject, eventdata, handles) % hObject handle to edit1 (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles empty - handles not created until after all CreateFcns called % Hint: edit controls usually have a white background on Windows. % See ISPC and COMPUTER. if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) set(hObject,'BackgroundColor','white'); end function edit3_Callback(hObject, eventdata, handles) % hObject handle to edit3 (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) % Hints: get(hObject,'String') returns contents of edit3 as text % str2double(get(hObject,'String')) returns contents of edit3 as a double % --- Executes during object creation, after setting all properties. function edit3_CreateFcn(hObject, eventdata, handles) % hObject handle to edit3 (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles empty - handles not created until after all CreateFcns called % Hint: edit controls usually have a white background on Windows. % See ISPC and COMPUTER. if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) set(hObject,'BackgroundColor','white'); end function edit4_Callback(hObject, eventdata, handles) % hObject handle to edit4 (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) % Hints: get(hObject,'String') returns contents of edit4 as text % str2double(get(hObject,'String')) returns contents of edit4 as a double % --- Executes during object creation, after setting all properties. function edit4_CreateFcn(hObject, eventdata, handles) % hObject handle to edit4 (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles empty - handles not created until after all CreateFcns called % Hint: edit controls usually have a white background on Windows. % See ISPC and COMPUTER. if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) set(hObject,'BackgroundColor','white'); end function edit5_Callback(hObject, eventdata, handles) % hObject handle to edit5 (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) % Hints: get(hObject,'String') returns contents of edit5 as text % str2double(get(hObject,'String')) returns contents of edit5 as a double % --- Executes during object creation, after setting all properties. function edit5_CreateFcn(hObject, eventdata, handles) % hObject handle to edit5 (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles empty - handles not created until after all CreateFcns called % Hint: edit controls usually have a white background on Windows. % See ISPC and COMPUTER. if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) set(hObject,'BackgroundColor','white'); end function edit6_Callback(hObject, eventdata, handles) % hObject handle to edit6 (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) % Hints: get(hObject,'String') returns contents of edit6 as text % str2double(get(hObject,'String')) returns contents of edit6 as a double % --- Executes during object creation, after setting all properties. function edit6_CreateFcn(hObject, eventdata, handles) % hObject handle to edit6 (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles empty - handles not created until after all CreateFcns called % Hint: edit controls usually have a white background on Windows. % See ISPC and COMPUTER. if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) set(hObject,'BackgroundColor','white'); end function edit7_Callback(hObject, eventdata, handles) % hObject handle to edit7 (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) % Hints: get(hObject,'String') returns contents of edit7 as text % str2double(get(hObject,'String')) returns contents of edit7 as a double % --- Executes during object creation, after setting all properties. function edit7_CreateFcn(hObject, eventdata, handles) % hObject handle to edit7 (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles empty - handles not created until after all CreateFcns called % Hint: edit controls usually have a white background on Windows. % See ISPC and COMPUTER. if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) set(hObject,'BackgroundColor','white'); end